source: src/molecule.hpp@ e87acf

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Last change on this file since e87acf was e87acf, checked in by Tillmann Crueger <crueger@…>, 16 years ago

BROKEN: removed legacy AtomList from molecule class
  • Property mode set to 100755
File size: 21.5 KB
Line 
1/** \file molecule.hpp
2 *
3 * Class definitions of atom and molecule, element and periodentafel
4 */
5
6#ifndef MOLECULES_HPP_
7#define MOLECULES_HPP_
8
9using namespace std;
10
11/*********************************************** includes ***********************************/
12
13// GSL headers
14#include <gsl/gsl_eigen.h>
15#include <gsl/gsl_heapsort.h>
16#include <gsl/gsl_linalg.h>
17#include <gsl/gsl_matrix.h>
18#include <gsl/gsl_multimin.h>
19#include <gsl/gsl_vector.h>
20#include <gsl/gsl_randist.h>
21
22//// STL headers
23#include <map>
24#include <set>
25#include <deque>
26#include <list>
27#include <vector>
28
29#include <string>
30
31#include "defs.hpp"
32#include "graph.hpp"
33#include "stackclass.hpp"
34#include "tesselation.hpp"
35#include "Patterns/Observer.hpp"
36#include "Patterns/ObservedIterator.hpp"
37#include "Patterns/Cacheable.hpp"
38
39/****************************************** forward declarations *****************************/
40
41class atom;
42class bond;
43class BondedParticle;
44class BondGraph;
45class element;
46class ForceMatrix;
47class LinkedCell;
48class molecule;
49class MoleculeLeafClass;
50class MoleculeListClass;
51class periodentafel;
52class Vector;
53
54/******************************** Some definitions for easier reading **********************************/
55
56#define MoleculeList list <molecule *>
57#define MoleculeListTest pair <MoleculeList::iterator, bool>
58
59#define DistancePair pair < double, atom* >
60#define DistanceMap multimap < double, atom* >
61#define DistanceTestPair pair < DistanceMap::iterator, bool>
62
63
64/************************************* Class definitions ****************************************/
65
66/** Structure to contain parameters needed for evaluation of constraint potential.
67 */
68struct EvaluatePotential
69{
70 int startstep; //!< start configuration (MDStep in atom::trajectory)
71 int endstep; //!< end configuration (MDStep in atom::trajectory)
72 atom **PermutationMap; //!< gives target ptr for each atom, array of size molecule::AtomCount (this is "x" in \f$ V^{con}(x) \f$ )
73 DistanceMap **DistanceList; //!< distance list of each atom to each atom
74 DistanceMap::iterator *StepList; //!< iterator to ascend through NearestNeighbours \a **DistanceList
75 int *DoubleList; //!< count of which sources want to move to this target, basically the injective measure (>1 -> not injective)
76 DistanceMap::iterator *DistanceIterators; //!< marks which was the last picked target as injective candidate with smallest distance
77 bool IsAngstroem; //!< whether coordinates are in angstroem (true) or bohrradius (false)
78 double *PenaltyConstants; //!< penalty constant in front of each term
79};
80
81#define MaxThermostats 6 //!< maximum number of thermostat entries in Ions#ThermostatNames and Ions#ThermostatImplemented
82enum thermostats { None, Woodcock, Gaussian, Langevin, Berendsen, NoseHoover }; //!< Thermostat names for output
83
84
85/** The complete molecule.
86 * Class incorporates number of types
87 */
88class molecule : public PointCloud , public Observable {
89 friend molecule *NewMolecule();
90 friend void DeleteMolecule(molecule *);
91
92 public:
93 typedef std::set<atom*> atomSet;
94 typedef ObservedIterator<atomSet> iterator;
95 typedef atomSet::const_iterator const_iterator;
96 double cell_size[6];//!< cell size
97 const periodentafel * const elemente; //!< periodic table with each element
98 // old deprecated atom handling
99 //atom *start; //!< start of atom list
100 //atom *end; //!< end of atom list
101 bond *first; //!< start of bond list
102 bond *last; //!< end of bond list
103 int MDSteps; //!< The number of MD steps in Trajectories
104 int AtomCount; //!< number of atoms, brought up-to-date by CountAtoms()
105 int BondCount; //!< number of atoms, brought up-to-date by CountBonds()
106 int ElementCount; //!< how many unique elements are therein
107 int ElementsInMolecule[MAX_ELEMENTS]; //!< list whether element (sorted by atomic number) is alread present or not
108 mutable int NoNonHydrogen; //!< number of non-hydrogen atoms in molecule
109 mutable int NoNonBonds; //!< number of non-hydrogen bonds in molecule
110 mutable int NoCyclicBonds; //!< number of cyclic bonds in molecule, by DepthFirstSearchAnalysis()
111 double BondDistance; //!< typical bond distance used in CreateAdjacencyList() and furtheron
112 bool ActiveFlag; //!< in a MoleculeListClass used to discern active from inactive molecules
113 Vector Center; //!< Center of molecule in a global box
114 int IndexNr; //!< index of molecule in a MoleculeListClass
115 char name[MAXSTRINGSIZE]; //!< arbitrary name
116
117 private:
118 Cacheable<string> formula;
119 moleculeId_t id;
120 atomSet atoms; //<!set of atoms
121 protected:
122 molecule(const periodentafel * const teil);
123 virtual ~molecule();
124
125
126public:
127 //getter and setter
128 const std::string getName();
129 moleculeId_t getId();
130 void setId(moleculeId_t);
131 void setName(const std::string);
132 const std::string getFormula();
133 std::string calcFormula();
134
135 iterator begin();
136 const_iterator begin() const;
137 iterator end();
138 const_iterator end() const;
139
140
141 // re-definition of virtual functions from PointCloud
142 const char * const GetName() const;
143 Vector *GetCenter() const ;
144 TesselPoint *GetPoint() const ;
145 TesselPoint *GetTerminalPoint() const ;
146 int GetMaxId() const;
147 void GoToNext() const ;
148 void GoToPrevious() const ;
149 void GoToFirst() const ;
150 void GoToLast() const ;
151 bool IsEmpty() const ;
152 bool IsEnd() const ;
153
154 // templates for allowing global manipulation of all vectors
155 template <typename res> void ActOnAllVectors( res (Vector::*f)() ) const;
156 template <typename res> void ActOnAllVectors( res (Vector::*f)() const) const;
157 template <typename res, typename T> void ActOnAllVectors( res (Vector::*f)(T), T t ) const;
158 template <typename res, typename T> void ActOnAllVectors( res (Vector::*f)(T) const, T t ) const;
159 template <typename res, typename T, typename U> void ActOnAllVectors( res (Vector::*f)(T, U), T t, U u ) const;
160 template <typename res, typename T, typename U> void ActOnAllVectors( res (Vector::*f)(T, U) const, T t, U u ) const;
161 template <typename res, typename T, typename U, typename V> void ActOnAllVectors( res (Vector::*f)(T, U, V), T t, U u, V v) const;
162 template <typename res, typename T, typename U, typename V> void ActOnAllVectors( res (Vector::*f)(T, U, V) const, T t, U u, V v) const;
163
164 // templates for allowing global manipulation of molecule with each atom as single argument
165 template <typename res> void ActWithEachAtom( res (molecule::*f)(atom *) ) const;
166 template <typename res> void ActWithEachAtom( res (molecule::*f)(atom *) const) const;
167
168 // templates for allowing global copying of molecule with each atom as single argument
169 template <typename res> void ActOnCopyWithEachAtom( res (molecule::*f)(atom *) , molecule *copy) const;
170 template <typename res> void ActOnCopyWithEachAtom( res (molecule::*f)(atom *) const, molecule *copy) const;
171
172 // templates for allowing global manipulation of all atoms
173 template <typename res, typename typ> void ActOnAllAtoms( res (typ::*f)() ) const;
174 template <typename res, typename typ> void ActOnAllAtoms( res (typ::*f)() const) const;
175 template <typename res, typename typ, typename T> void ActOnAllAtoms( res (typ::*f)(T), T t ) const;
176 template <typename res, typename typ, typename T> void ActOnAllAtoms( res (typ::*f)(T) const, T t ) const;
177 template <typename res, typename typ, typename T, typename U> void ActOnAllAtoms( res (typ::*f)(T, U), T t, U u ) const;
178 template <typename res, typename typ, typename T, typename U> void ActOnAllAtoms( res (typ::*f)(T, U) const, T t, U u ) const;
179 template <typename res, typename typ, typename T, typename U, typename V> void ActOnAllAtoms( res (typ::*f)(T, U, V), T t, U u, V v) const;
180 template <typename res, typename typ, typename T, typename U, typename V> void ActOnAllAtoms( res (typ::*f)(T, U, V) const, T t, U u, V v) const;
181 template <typename res, typename typ, typename T, typename U, typename V, typename W> void ActOnAllAtoms( res (typ::*f)(T, U, V, W), T t, U u, V v, W w) const;
182 template <typename res, typename typ, typename T, typename U, typename V, typename W> void ActOnAllAtoms( res (typ::*f)(T, U, V, W) const, T t, U u, V v, W w) const;
183
184 // templates for allowing conditional global copying of molecule with each atom as single argument
185 template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) () ) const;
186 template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) () const ) const;
187 template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) () ) const;
188 template <typename res> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) () const ) const;
189 template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) (T), T t ) const;
190 template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) (T) const, T t ) const;
191 template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) (T), T t ) const;
192 template <typename res, typename T> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) (T) const, T t ) const;
193 template <typename res, typename T, typename U> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) (T, U), T t, U u ) const;
194 template <typename res, typename T, typename U> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) (T, U) const, T t, U u ) const;
195 template <typename res, typename T, typename U> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) (T, U), T t, U u ) const;
196 template <typename res, typename T, typename U> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) (T, U) const, T t, U u ) const;
197 template <typename res, typename T, typename U, typename V> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) (T, U, V), T t, U u, V v ) const;
198 template <typename res, typename T, typename U, typename V> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) , molecule *copy, bool (atom::*condition) (T, U, V) const, T t, U u, V v ) const;
199 template <typename res, typename T, typename U, typename V> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) (T, U, V), T t, U u, V v ) const;
200 template <typename res, typename T, typename U, typename V> void ActOnCopyWithEachAtomIfTrue( res (molecule::*f)(atom *) const , molecule *copy, bool (atom::*condition) (T, U, V) const, T t, U u, V v ) const;
201
202 // templates for allowing global manipulation of an array with one entry per atom
203 void SetIndexedArrayForEachAtomTo ( atom **array, int ParticleInfo::* index) const;
204 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::* index, void (*Setor)(T *, T *)) const;
205 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::* index, void (*Setor)(T *, T *), T t) const;
206 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::* index, void (*Setor)(T *, T *), T *t) const;
207 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int element::* index, void (*Setor)(T *, T *)) const;
208 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int element::* index, void (*Setor)(T *, T *), T t) const;
209 template <typename T> void SetIndexedArrayForEachAtomTo ( T *array, int element::* index, void (*Setor)(T *, T *), T *t) const;
210 template <typename T, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &), typ atom::*value) const;
211 template <typename T, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &) const, typ atom::*value) const;
212 template <typename T, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &), typ &vect ) const;
213 template <typename T, typename typ> void SetIndexedArrayForEachAtomTo ( T *array, int ParticleInfo::*index, T (atom::*Setor)(typ &) const, typ &vect ) const;
214
215 // templates for allowing global manipulation of each atom by entries in an array
216 template <typename T, typename typ, typename typ2> void SetAtomValueToIndexedArray ( T *array, int typ::*index, T typ2::*value ) const;
217 template <typename T, typename typ> void SetAtomValueToValue ( T value, T typ::*ptr ) const;
218
219 template <typename res, typename typ> res SumPerAtom(res (typ::*f)() ) const;
220 template <typename res, typename typ> res SumPerAtom(res (typ::*f)() const ) const;
221 template <typename res, typename typ, typename T> res SumPerAtom(res (typ::*f)(T) , T t ) const;
222 template <typename res, typename typ, typename T> res SumPerAtom(res (typ::*f)(T) const, T t ) const;
223
224 /// remove atoms from molecule.
225 bool AddAtom(atom *pointer);
226 bool RemoveAtom(atom *pointer);
227 bool UnlinkAtom(atom *pointer);
228 bool CleanupMolecule();
229
230 /// Add/remove atoms to/from molecule.
231 atom * AddCopyAtom(atom *pointer);
232 bool AddXYZFile(string filename);
233 bool AddHydrogenReplacementAtom(bond *Bond, atom *BottomOrigin, atom *TopOrigin, atom *TopReplacement, bool IsAngstroem);
234 bond * AddBond(atom *first, atom *second, int degree = 1);
235 bool RemoveBond(bond *pointer);
236 bool RemoveBonds(atom *BondPartner);
237
238 /// Find atoms.
239 atom * FindAtom(int Nr) const;
240 atom * AskAtom(string text);
241
242 /// Count and change present atoms' coordination.
243 void CountAtoms();
244 void CountElements();
245 void CalculateOrbitals(class config &configuration);
246 bool CenterInBox();
247 bool BoundInBox();
248 void CenterEdge(Vector *max);
249 void CenterOrigin();
250 void CenterPeriodic();
251 void CenterAtVector(Vector *newcenter);
252 void Translate(const Vector *x);
253 void TranslatePeriodically(const Vector *trans);
254 void Mirror(const Vector *x);
255 void Align(Vector *n);
256 void Scale(const double ** const factor);
257 void DeterminePeriodicCenter(Vector &center);
258 Vector * DetermineCenterOfGravity();
259 Vector * DetermineCenterOfAll() const;
260 void SetNameFromFilename(const char *filename);
261 void SetBoxDimension(Vector *dim);
262 void ScanForPeriodicCorrection();
263 bool VerletForceIntegration(char *file, config &configuration);
264 void Thermostats(config &configuration, double ActualTemp, int Thermostat);
265 void PrincipalAxisSystem(bool DoRotate);
266 double VolumeOfConvexEnvelope(bool IsAngstroem);
267
268 double ConstrainedPotential(struct EvaluatePotential &Params);
269 double MinimiseConstrainedPotential(atom **&permutation, int startstep, int endstep, bool IsAngstroem);
270 void EvaluateConstrainedForces(int startstep, int endstep, atom **PermutationMap, ForceMatrix *Force);
271 bool LinearInterpolationBetweenConfiguration(int startstep, int endstep, const char *prefix, config &configuration, bool MapByIdentity);
272
273 bool CheckBounds(const Vector *x) const;
274 void GetAlignvector(struct lsq_params * par) const;
275
276 /// Initialising routines in fragmentation
277 void CreateAdjacencyListFromDbondFile(ifstream *output);
278 void CreateAdjacencyList(double bonddistance, bool IsAngstroem, void (BondGraph::*f)(BondedParticle * const , BondedParticle * const , double &, double &, bool), BondGraph *BG = NULL);
279 int CorrectBondDegree() const;
280 void OutputBondsList() const;
281 void CyclicBondAnalysis() const;
282 void OutputGraphInfoPerAtom() const;
283 void OutputGraphInfoPerBond() const;
284
285
286 // Graph analysis
287 MoleculeLeafClass * DepthFirstSearchAnalysis(class StackClass<bond *> *&BackEdgeStack) const;
288 void CyclicStructureAnalysis(class StackClass<bond *> *BackEdgeStack, int *&MinimumRingSize) const;
289 bool PickLocalBackEdges(atom **ListOfLocalAtoms, class StackClass<bond *> *&ReferenceStack, class StackClass<bond *> *&LocalStack) const;
290 bond * FindNextUnused(atom *vertex) const;
291 void SetNextComponentNumber(atom *vertex, int nr) const;
292 void ResetAllBondsToUnused() const;
293 int CountCyclicBonds();
294 bool CheckForConnectedSubgraph(KeySet *Fragment);
295 string GetColor(enum Shading color) const;
296 bond * CopyBond(atom *left, atom *right, bond *CopyBond);
297
298
299 molecule *CopyMolecule();
300 molecule* CopyMoleculeFromSubRegion(const Vector offset, const double *parallelepiped) const;
301
302 /// Fragment molecule by two different approaches:
303 int FragmentMolecule(int Order, config *configuration);
304 bool CheckOrderAtSite(bool *AtomMask, Graph *GlobalKeySetList, int Order, int *MinimumRingSize, char *path = NULL);
305 bool StoreBondsToFile(char *path);
306 bool StoreAdjacencyToFile(char *path);
307 bool CheckAdjacencyFileAgainstMolecule(char *path, atom **ListOfAtoms);
308 bool ParseOrderAtSiteFromFile(char *path);
309 bool StoreOrderAtSiteFile(char *path);
310 bool StoreForcesFile(MoleculeListClass *BondFragments, char *path, int *SortIndex);
311 bool CreateMappingLabelsToConfigSequence(int *&SortIndex);
312 void BreadthFirstSearchAdd(molecule *Mol, atom **&AddedAtomList, bond **&AddedBondList, atom *Root, bond *Bond, int BondOrder, bool IsAngstroem);
313 /// -# BOSSANOVA
314 void FragmentBOSSANOVA(Graph *&FragmentList, KeyStack &RootStack, int *MinimumRingSize);
315 int PowerSetGenerator(int Order, struct UniqueFragments &FragmentSearch, KeySet RestrictedKeySet);
316 bool BuildInducedSubgraph(const molecule *Father);
317 molecule * StoreFragmentFromKeySet(KeySet &Leaflet, bool IsAngstroem);
318 void SPFragmentGenerator(struct UniqueFragments *FragmentSearch, int RootDistance, bond **BondsSet, int SetDimension, int SubOrder);
319 int LookForRemovalCandidate(KeySet *&Leaf, int *&ShortestPathList);
320 int GuesstimateFragmentCount(int order);
321
322 // Recognize doubly appearing molecules in a list of them
323 int * IsEqualToWithinThreshold(molecule *OtherMolecule, double threshold);
324 int * GetFatherSonAtomicMap(molecule *OtherMolecule);
325
326 // Output routines.
327 bool Output(ofstream * const output);
328 bool OutputTrajectories(ofstream * const output);
329 void OutputListOfBonds() const;
330 bool OutputXYZ(ofstream * const output) const;
331 bool OutputTrajectoriesXYZ(ofstream * const output);
332 bool Checkout(ofstream * const output) const;
333 bool OutputTemperatureFromTrajectories(ofstream * const output, int startstep, int endstep);
334
335 // Manipulation routines
336 void flipActiveFlag();
337
338 private:
339 int last_atom; //!< number given to last atom
340 mutable atom *InternalPointer; //!< internal pointer for PointCloud
341};
342
343molecule *NewMolecule();
344void DeleteMolecule(molecule* mol);
345
346#include "molecule_template.hpp"
347
348/** A list of \a molecule classes.
349 */
350class MoleculeListClass : public Observable {
351 public:
352 MoleculeList ListOfMolecules; //!< List of the contained molecules
353 int MaxIndex;
354
355 MoleculeListClass(World *world);
356 ~MoleculeListClass();
357
358 bool AddHydrogenCorrection(char *path);
359 bool StoreForcesFile(char *path, int *SortIndex);
360 void insert(molecule *mol);
361 molecule * ReturnIndex(int index);
362 bool OutputConfigForListOfFragments(config *configuration, int *SortIndex);
363 int NumberOfActiveMolecules();
364 void Enumerate(ostream *out);
365 void Output(ofstream *out);
366 void DissectMoleculeIntoConnectedSubgraphs(const periodentafel * const periode, config * const configuration);
367 int CountAllAtoms() const;
368
369 // Methods moved here from the menus
370 // TODO: more refactoring needed on these methods
371 void flipChosen();
372 void createNewMolecule(periodentafel *periode);
373 void loadFromXYZ(periodentafel *periode);
374 void setMoleculeFilename();
375 void parseXYZIntoMolecule();
376 void eraseMolecule();
377
378
379 // merging of molecules
380 bool SimpleMerge(molecule *mol, molecule *srcmol);
381 bool SimpleAdd(molecule *mol, molecule *srcmol);
382 bool SimpleMultiMerge(molecule *mol, int *src, int N);
383 bool SimpleMultiAdd(molecule *mol, int *src, int N);
384 bool ScatterMerge(molecule *mol, int *src, int N);
385 bool EmbedMerge(molecule *mol, molecule *srcmol);
386
387 private:
388 World *world; //!< The world this List belongs to. Needed to avoid deadlocks in the destructor
389};
390
391
392/** A leaf for a tree of \a molecule class
393 * Wraps molecules in a tree structure
394 */
395class MoleculeLeafClass {
396 public:
397 molecule *Leaf; //!< molecule of this leaf
398 //MoleculeLeafClass *UpLeaf; //!< Leaf one level up
399 //MoleculeLeafClass *DownLeaf; //!< First leaf one level down
400 MoleculeLeafClass *previous; //!< Previous leaf on this level
401 MoleculeLeafClass *next; //!< Next leaf on this level
402
403 //MoleculeLeafClass(MoleculeLeafClass *Up, MoleculeLeafClass *Previous);
404 MoleculeLeafClass(MoleculeLeafClass *PreviousLeaf);
405 ~MoleculeLeafClass();
406
407 bool AddLeaf(molecule *ptr, MoleculeLeafClass *Previous);
408 bool FillBondStructureFromReference(const molecule * const reference, int &FragmentCounter, atom ***&ListOfLocalAtoms, bool FreeList = false);
409 bool FillRootStackForSubgraphs(KeyStack *&RootStack, bool *AtomMask, int &FragmentCounter);
410 bool AssignKeySetsToFragment(molecule *reference, Graph *KeySetList, atom ***&ListOfLocalAtoms, Graph **&FragmentList, int &FragmentCounter, bool FreeList = false);
411 bool FillListOfLocalAtoms(atom ***&ListOfLocalAtoms, const int FragmentCounter, const int GlobalAtomCount, bool &FreeList);
412 void TranslateIndicesToGlobalIDs(Graph **FragmentList, int &FragmentCounter, int &TotalNumberOfKeySets, Graph &TotalGraph);
413 int Count() const;
414};
415
416
417#endif /*MOLECULES_HPP_*/
418
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